Multiple sequence alignment - TraesCS3D01G450300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G450300 chr3D 100.000 2719 0 0 1 2719 558661546 558664264 0.000000e+00 5022.0
1 TraesCS3D01G450300 chr3D 84.132 605 84 4 987 1591 558709027 558708435 2.350000e-160 575.0
2 TraesCS3D01G450300 chr3D 92.473 279 18 3 2168 2444 133221037 133221314 1.960000e-106 396.0
3 TraesCS3D01G450300 chr3D 90.747 281 16 4 2439 2719 133265176 133265446 1.540000e-97 366.0
4 TraesCS3D01G450300 chr3D 85.816 282 15 12 654 921 558709297 558709027 2.670000e-70 276.0
5 TraesCS3D01G450300 chr3D 78.932 337 61 9 105 435 147450909 147450577 1.270000e-53 220.0
6 TraesCS3D01G450300 chr3D 83.568 213 28 6 2426 2634 182220628 182220419 2.760000e-45 193.0
7 TraesCS3D01G450300 chr3A 91.127 1296 49 10 648 1910 694990121 694988859 0.000000e+00 1696.0
8 TraesCS3D01G450300 chr3A 90.476 651 43 8 3 649 694990860 694990225 0.000000e+00 841.0
9 TraesCS3D01G450300 chr3A 83.802 605 82 5 987 1591 695021289 695020701 6.570000e-156 560.0
10 TraesCS3D01G450300 chr3A 82.746 284 30 10 654 921 695021569 695021289 4.530000e-58 235.0
11 TraesCS3D01G450300 chr3A 92.157 153 7 3 1986 2137 694988607 694988459 7.630000e-51 211.0
12 TraesCS3D01G450300 chr3A 80.930 215 30 9 2426 2634 683037758 683037967 2.800000e-35 159.0
13 TraesCS3D01G450300 chr3B 90.000 1330 52 21 639 1923 741352832 741351539 0.000000e+00 1644.0
14 TraesCS3D01G450300 chr3B 82.397 943 121 14 654 1586 741384935 741384028 0.000000e+00 780.0
15 TraesCS3D01G450300 chr3B 94.886 176 2 3 1995 2167 741351271 741351100 4.460000e-68 268.0
16 TraesCS3D01G450300 chr3B 78.487 423 76 11 24 435 215101178 215101596 2.080000e-66 263.0
17 TraesCS3D01G450300 chr3B 74.414 469 110 10 62 524 19161654 19161190 2.760000e-45 193.0
18 TraesCS3D01G450300 chr4A 84.280 528 77 6 1 524 617582711 617582186 6.720000e-141 510.0
19 TraesCS3D01G450300 chr4A 83.871 217 27 7 2426 2637 620027289 620027076 1.650000e-47 200.0
20 TraesCS3D01G450300 chr4A 82.500 200 23 9 2426 2620 698875138 698874946 6.020000e-37 165.0
21 TraesCS3D01G450300 chr7B 83.220 441 70 4 3 440 601385452 601385891 4.220000e-108 401.0
22 TraesCS3D01G450300 chr7B 83.158 190 26 5 2451 2636 634773095 634772908 4.660000e-38 169.0
23 TraesCS3D01G450300 chr5B 92.713 247 17 1 2314 2560 452230346 452230101 3.330000e-94 355.0
24 TraesCS3D01G450300 chr5B 83.019 212 27 7 2426 2632 692888550 692888343 1.660000e-42 183.0
25 TraesCS3D01G450300 chr5B 88.312 154 10 2 2564 2717 452229713 452229568 7.740000e-41 178.0
26 TraesCS3D01G450300 chr2D 74.735 471 102 16 60 521 143328251 143328713 7.680000e-46 195.0
27 TraesCS3D01G450300 chr2D 92.857 84 5 1 2166 2249 644290124 644290206 1.320000e-23 121.0
28 TraesCS3D01G450300 chr2D 90.217 92 8 1 2167 2257 284971066 284971157 4.760000e-23 119.0
29 TraesCS3D01G450300 chr5A 82.629 213 30 6 2426 2634 52737492 52737701 5.980000e-42 182.0
30 TraesCS3D01G450300 chr1B 87.234 141 11 2 2525 2665 641517387 641517520 1.300000e-33 154.0
31 TraesCS3D01G450300 chr6D 73.183 399 97 9 60 452 336461264 336460870 4.720000e-28 135.0
32 TraesCS3D01G450300 chr6D 90.110 91 8 1 2169 2258 38161686 38161776 1.710000e-22 117.0
33 TraesCS3D01G450300 chr6D 72.403 308 67 16 90 389 370579542 370579839 6.240000e-12 82.4
34 TraesCS3D01G450300 chr4D 92.391 92 6 1 2168 2258 492845878 492845969 2.200000e-26 130.0
35 TraesCS3D01G450300 chr4D 81.481 135 15 9 322 451 4484167 4484296 4.790000e-18 102.0
36 TraesCS3D01G450300 chr2B 97.333 75 2 0 2165 2239 133686363 133686289 7.900000e-26 128.0
37 TraesCS3D01G450300 chr7D 91.209 91 6 2 2160 2249 138275899 138275810 3.680000e-24 122.0
38 TraesCS3D01G450300 chr7D 91.209 91 7 1 2169 2258 604536036 604535946 3.680000e-24 122.0
39 TraesCS3D01G450300 chr6A 90.110 91 7 2 2169 2258 605280913 605281002 1.710000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G450300 chr3D 558661546 558664264 2718 False 5022.0 5022 100.000000 1 2719 1 chr3D.!!$F3 2718
1 TraesCS3D01G450300 chr3D 558708435 558709297 862 True 425.5 575 84.974000 654 1591 2 chr3D.!!$R3 937
2 TraesCS3D01G450300 chr3A 694988459 694990860 2401 True 916.0 1696 91.253333 3 2137 3 chr3A.!!$R1 2134
3 TraesCS3D01G450300 chr3A 695020701 695021569 868 True 397.5 560 83.274000 654 1591 2 chr3A.!!$R2 937
4 TraesCS3D01G450300 chr3B 741351100 741352832 1732 True 956.0 1644 92.443000 639 2167 2 chr3B.!!$R3 1528
5 TraesCS3D01G450300 chr3B 741384028 741384935 907 True 780.0 780 82.397000 654 1586 1 chr3B.!!$R2 932
6 TraesCS3D01G450300 chr4A 617582186 617582711 525 True 510.0 510 84.280000 1 524 1 chr4A.!!$R1 523
7 TraesCS3D01G450300 chr5B 452229568 452230346 778 True 266.5 355 90.512500 2314 2717 2 chr5B.!!$R2 403

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
923 1065 0.032678 CTTCGGAGATCATCGGTGGG 59.967 60.0 0.0 0.0 35.04 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2826 0.03467 AGATGCTGGCTGGAAGGTTC 60.035 55.0 0.0 0.0 0.0 3.62 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 3.785859 GCTCCATCGGGTCCAGCA 61.786 66.667 0.00 0.00 33.03 4.41
210 211 1.008327 TGATCCAGTAGCCCTCCTTCA 59.992 52.381 0.00 0.00 0.00 3.02
217 218 2.034221 GCCCTCCTTCACGGCTTT 59.966 61.111 0.00 0.00 39.70 3.51
273 274 1.225855 CGCCACAGTACTTTGCTTCA 58.774 50.000 3.35 0.00 0.00 3.02
290 291 4.218417 TGCTTCAAATTCTTCCAGCTTACC 59.782 41.667 0.00 0.00 0.00 2.85
291 292 4.218417 GCTTCAAATTCTTCCAGCTTACCA 59.782 41.667 0.00 0.00 0.00 3.25
299 301 2.114670 CCAGCTTACCATGCCACCG 61.115 63.158 0.00 0.00 0.00 4.94
345 347 9.597170 CTGATTGAGATCTAAAGTCATCTGAAA 57.403 33.333 0.00 0.00 27.91 2.69
396 401 4.460263 ACTTTACAATGAGCACTTCACCA 58.540 39.130 0.00 0.00 38.99 4.17
408 416 4.037923 AGCACTTCACCACCAAATACAAAG 59.962 41.667 0.00 0.00 0.00 2.77
409 417 4.037446 GCACTTCACCACCAAATACAAAGA 59.963 41.667 0.00 0.00 0.00 2.52
410 418 5.451242 GCACTTCACCACCAAATACAAAGAA 60.451 40.000 0.00 0.00 0.00 2.52
411 419 6.738453 GCACTTCACCACCAAATACAAAGAAT 60.738 38.462 0.00 0.00 0.00 2.40
531 539 3.551046 CGTAGGACACATCTGGTATCTGC 60.551 52.174 0.00 0.00 0.00 4.26
532 540 2.756907 AGGACACATCTGGTATCTGCT 58.243 47.619 0.00 0.00 0.00 4.24
533 541 2.697751 AGGACACATCTGGTATCTGCTC 59.302 50.000 0.00 0.00 0.00 4.26
534 542 2.544694 GGACACATCTGGTATCTGCTCG 60.545 54.545 0.00 0.00 0.00 5.03
535 543 2.099921 GACACATCTGGTATCTGCTCGT 59.900 50.000 0.00 0.00 0.00 4.18
536 544 3.288092 ACACATCTGGTATCTGCTCGTA 58.712 45.455 0.00 0.00 0.00 3.43
537 545 3.699538 ACACATCTGGTATCTGCTCGTAA 59.300 43.478 0.00 0.00 0.00 3.18
538 546 4.045104 CACATCTGGTATCTGCTCGTAAC 58.955 47.826 0.00 0.00 0.00 2.50
539 547 3.699538 ACATCTGGTATCTGCTCGTAACA 59.300 43.478 0.00 0.00 0.00 2.41
540 548 4.342378 ACATCTGGTATCTGCTCGTAACAT 59.658 41.667 0.00 0.00 0.00 2.71
541 549 5.163405 ACATCTGGTATCTGCTCGTAACATT 60.163 40.000 0.00 0.00 0.00 2.71
547 555 5.234543 GGTATCTGCTCGTAACATTTCCTTC 59.765 44.000 0.00 0.00 0.00 3.46
552 560 3.334691 CTCGTAACATTTCCTTCAGGCA 58.665 45.455 0.00 0.00 34.44 4.75
591 599 2.412325 CGTTGTCCGCTGTCCATTTTAC 60.412 50.000 0.00 0.00 0.00 2.01
592 600 2.812011 GTTGTCCGCTGTCCATTTTACT 59.188 45.455 0.00 0.00 0.00 2.24
593 601 3.134574 TGTCCGCTGTCCATTTTACTT 57.865 42.857 0.00 0.00 0.00 2.24
594 602 3.482436 TGTCCGCTGTCCATTTTACTTT 58.518 40.909 0.00 0.00 0.00 2.66
596 604 3.078837 TCCGCTGTCCATTTTACTTTCC 58.921 45.455 0.00 0.00 0.00 3.13
600 608 4.556233 GCTGTCCATTTTACTTTCCCAAC 58.444 43.478 0.00 0.00 0.00 3.77
613 621 1.475403 TCCCAACCGAACAAAAAGCA 58.525 45.000 0.00 0.00 0.00 3.91
626 634 7.290118 CGAACAAAAAGCAAATAAAATCCAGG 58.710 34.615 0.00 0.00 0.00 4.45
634 642 4.625311 GCAAATAAAATCCAGGTCCGTTTG 59.375 41.667 0.00 0.00 0.00 2.93
757 873 0.970427 AATCGGTTGGGTTGGCCATC 60.970 55.000 6.09 5.53 36.17 3.51
921 1063 2.359214 TCTTCTTCGGAGATCATCGGTG 59.641 50.000 0.00 0.00 35.04 4.94
922 1064 1.032794 TCTTCGGAGATCATCGGTGG 58.967 55.000 0.00 0.00 35.04 4.61
923 1065 0.032678 CTTCGGAGATCATCGGTGGG 59.967 60.000 0.00 0.00 35.04 4.61
924 1066 2.028125 TTCGGAGATCATCGGTGGGC 62.028 60.000 0.00 0.00 35.04 5.36
925 1067 2.029666 GGAGATCATCGGTGGGCG 59.970 66.667 0.00 0.00 0.00 6.13
926 1068 2.029666 GAGATCATCGGTGGGCGG 59.970 66.667 0.00 0.00 0.00 6.13
927 1069 4.241555 AGATCATCGGTGGGCGGC 62.242 66.667 0.00 0.00 0.00 6.53
1002 1144 3.794564 TCGGTTTTGATACGATCGACATG 59.205 43.478 24.34 4.25 0.00 3.21
1003 1145 3.060540 CGGTTTTGATACGATCGACATGG 60.061 47.826 24.34 0.00 0.00 3.66
1004 1146 3.303132 GGTTTTGATACGATCGACATGGC 60.303 47.826 24.34 10.44 0.00 4.40
1008 1150 3.817274 TACGATCGACATGGCGGCG 62.817 63.158 27.33 27.33 36.25 6.46
1069 1211 2.976350 TCGTGGTGCTCGTCGTCT 60.976 61.111 0.00 0.00 0.00 4.18
1128 1270 3.692406 AAGGTCGGCGGTCCTGAC 61.692 66.667 20.85 5.57 36.13 3.51
1379 1528 0.550914 TCAAGGTGAGCAAGGTTGGT 59.449 50.000 0.00 0.00 42.35 3.67
1494 1643 2.454832 CTTCGCCAGCTCCAACCTCA 62.455 60.000 0.00 0.00 0.00 3.86
1715 1882 0.034186 TGGTCCTGGCCTGCTTTATG 60.034 55.000 3.32 0.00 0.00 1.90
1756 1923 9.309516 TGTAGGCTAAAATAATTGACTAGTTCG 57.690 33.333 0.00 0.00 0.00 3.95
1835 2017 2.283351 GGTTTGATGTATCGTGTACCGC 59.717 50.000 0.00 0.00 36.19 5.68
1848 2034 0.458889 GTACCGCCTTCGCATGTGTA 60.459 55.000 6.09 0.00 34.03 2.90
1899 2086 3.654414 ACTTTGTGTCTCTGTTCGATCC 58.346 45.455 0.00 0.00 0.00 3.36
1960 2465 9.471084 CAAAGGGTAAATTTTACAACTTACAGG 57.529 33.333 18.41 9.96 0.00 4.00
1971 2476 5.514274 ACAACTTACAGGTGAACAATTGG 57.486 39.130 10.83 0.00 33.95 3.16
1976 2483 7.916914 ACTTACAGGTGAACAATTGGTATAC 57.083 36.000 10.83 6.12 0.00 1.47
2032 2581 1.968417 CGTCAGTTACGCACGTACG 59.032 57.895 15.01 15.01 46.10 3.67
2033 2582 0.722469 CGTCAGTTACGCACGTACGT 60.722 55.000 19.01 19.01 46.10 3.57
2045 2594 2.809601 GTACGTGTGCCCGCTCAG 60.810 66.667 0.00 0.00 0.00 3.35
2133 2682 5.822204 TCTGTAGCCCCTTTGCTTTATTAA 58.178 37.500 0.00 0.00 42.75 1.40
2167 2719 5.819991 TCCAGAATTAGTTCTTTGAGGCAT 58.180 37.500 0.00 0.00 41.92 4.40
2168 2720 6.957631 TCCAGAATTAGTTCTTTGAGGCATA 58.042 36.000 0.00 0.00 41.92 3.14
2169 2721 7.577303 TCCAGAATTAGTTCTTTGAGGCATAT 58.423 34.615 0.00 0.00 41.92 1.78
2170 2722 7.716998 TCCAGAATTAGTTCTTTGAGGCATATC 59.283 37.037 0.00 0.00 41.92 1.63
2171 2723 7.718753 CCAGAATTAGTTCTTTGAGGCATATCT 59.281 37.037 0.00 0.00 41.92 1.98
2172 2724 9.770097 CAGAATTAGTTCTTTGAGGCATATCTA 57.230 33.333 0.00 0.00 41.92 1.98
2198 2750 7.707467 AATACCTAAATAGTTCATCCCCACT 57.293 36.000 0.00 0.00 0.00 4.00
2199 2751 8.808240 AATACCTAAATAGTTCATCCCCACTA 57.192 34.615 0.00 0.00 0.00 2.74
2200 2752 8.990693 ATACCTAAATAGTTCATCCCCACTAT 57.009 34.615 0.00 0.00 37.75 2.12
2201 2753 7.079451 ACCTAAATAGTTCATCCCCACTATG 57.921 40.000 0.00 0.00 36.52 2.23
2202 2754 5.940470 CCTAAATAGTTCATCCCCACTATGC 59.060 44.000 0.00 0.00 36.52 3.14
2203 2755 5.653255 AAATAGTTCATCCCCACTATGCT 57.347 39.130 0.00 0.00 36.52 3.79
2204 2756 6.763715 AAATAGTTCATCCCCACTATGCTA 57.236 37.500 0.00 0.00 36.52 3.49
2205 2757 6.959606 AATAGTTCATCCCCACTATGCTAT 57.040 37.500 0.00 0.00 36.52 2.97
2206 2758 6.959606 ATAGTTCATCCCCACTATGCTATT 57.040 37.500 0.00 0.00 35.32 1.73
2207 2759 5.653255 AGTTCATCCCCACTATGCTATTT 57.347 39.130 0.00 0.00 0.00 1.40
2208 2760 5.625150 AGTTCATCCCCACTATGCTATTTC 58.375 41.667 0.00 0.00 0.00 2.17
2209 2761 5.370880 AGTTCATCCCCACTATGCTATTTCT 59.629 40.000 0.00 0.00 0.00 2.52
2210 2762 5.233083 TCATCCCCACTATGCTATTTCTG 57.767 43.478 0.00 0.00 0.00 3.02
2211 2763 4.660303 TCATCCCCACTATGCTATTTCTGT 59.340 41.667 0.00 0.00 0.00 3.41
2212 2764 5.132648 TCATCCCCACTATGCTATTTCTGTT 59.867 40.000 0.00 0.00 0.00 3.16
2213 2765 4.780815 TCCCCACTATGCTATTTCTGTTG 58.219 43.478 0.00 0.00 0.00 3.33
2214 2766 4.473196 TCCCCACTATGCTATTTCTGTTGA 59.527 41.667 0.00 0.00 0.00 3.18
2215 2767 4.576463 CCCCACTATGCTATTTCTGTTGAC 59.424 45.833 0.00 0.00 0.00 3.18
2216 2768 5.185454 CCCACTATGCTATTTCTGTTGACA 58.815 41.667 0.00 0.00 0.00 3.58
2217 2769 5.824624 CCCACTATGCTATTTCTGTTGACAT 59.175 40.000 0.00 0.00 0.00 3.06
2218 2770 6.238566 CCCACTATGCTATTTCTGTTGACATG 60.239 42.308 0.00 0.00 0.00 3.21
2219 2771 6.197276 CACTATGCTATTTCTGTTGACATGC 58.803 40.000 0.00 0.00 0.00 4.06
2220 2772 5.882000 ACTATGCTATTTCTGTTGACATGCA 59.118 36.000 0.00 0.00 0.00 3.96
2221 2773 4.690184 TGCTATTTCTGTTGACATGCAG 57.310 40.909 0.00 0.00 0.00 4.41
2222 2774 3.119743 TGCTATTTCTGTTGACATGCAGC 60.120 43.478 0.00 0.00 33.09 5.25
2223 2775 3.733077 GCTATTTCTGTTGACATGCAGCC 60.733 47.826 0.00 0.00 33.09 4.85
2224 2776 1.985473 TTTCTGTTGACATGCAGCCT 58.015 45.000 0.00 0.00 33.09 4.58
2225 2777 2.857186 TTCTGTTGACATGCAGCCTA 57.143 45.000 0.00 0.00 33.09 3.93
2226 2778 3.354948 TTCTGTTGACATGCAGCCTAT 57.645 42.857 0.00 0.00 33.09 2.57
2227 2779 2.910199 TCTGTTGACATGCAGCCTATC 58.090 47.619 0.00 0.00 33.09 2.08
2228 2780 1.945394 CTGTTGACATGCAGCCTATCC 59.055 52.381 0.00 0.00 0.00 2.59
2229 2781 1.281577 TGTTGACATGCAGCCTATCCA 59.718 47.619 0.00 0.00 0.00 3.41
2230 2782 1.672881 GTTGACATGCAGCCTATCCAC 59.327 52.381 0.00 0.00 0.00 4.02
2231 2783 0.911053 TGACATGCAGCCTATCCACA 59.089 50.000 0.00 0.00 0.00 4.17
2232 2784 1.491754 TGACATGCAGCCTATCCACAT 59.508 47.619 0.00 0.00 0.00 3.21
2233 2785 2.149578 GACATGCAGCCTATCCACATC 58.850 52.381 0.00 0.00 0.00 3.06
2234 2786 1.491754 ACATGCAGCCTATCCACATCA 59.508 47.619 0.00 0.00 0.00 3.07
2235 2787 2.107726 ACATGCAGCCTATCCACATCAT 59.892 45.455 0.00 0.00 0.00 2.45
2236 2788 2.556144 TGCAGCCTATCCACATCATC 57.444 50.000 0.00 0.00 0.00 2.92
2237 2789 1.770061 TGCAGCCTATCCACATCATCA 59.230 47.619 0.00 0.00 0.00 3.07
2238 2790 2.224450 TGCAGCCTATCCACATCATCAG 60.224 50.000 0.00 0.00 0.00 2.90
2239 2791 2.224475 GCAGCCTATCCACATCATCAGT 60.224 50.000 0.00 0.00 0.00 3.41
2240 2792 3.007290 GCAGCCTATCCACATCATCAGTA 59.993 47.826 0.00 0.00 0.00 2.74
2241 2793 4.564041 CAGCCTATCCACATCATCAGTAC 58.436 47.826 0.00 0.00 0.00 2.73
2242 2794 3.256879 AGCCTATCCACATCATCAGTACG 59.743 47.826 0.00 0.00 0.00 3.67
2243 2795 3.005897 GCCTATCCACATCATCAGTACGT 59.994 47.826 0.00 0.00 0.00 3.57
2244 2796 4.799678 CCTATCCACATCATCAGTACGTC 58.200 47.826 0.00 0.00 0.00 4.34
2245 2797 3.735237 ATCCACATCATCAGTACGTCC 57.265 47.619 0.00 0.00 0.00 4.79
2246 2798 1.754803 TCCACATCATCAGTACGTCCC 59.245 52.381 0.00 0.00 0.00 4.46
2247 2799 1.480545 CCACATCATCAGTACGTCCCA 59.519 52.381 0.00 0.00 0.00 4.37
2248 2800 2.540515 CACATCATCAGTACGTCCCAC 58.459 52.381 0.00 0.00 0.00 4.61
2260 2812 2.936050 CGTCCCACGTGTAAAAACTC 57.064 50.000 15.65 0.00 36.74 3.01
2261 2813 1.528161 CGTCCCACGTGTAAAAACTCC 59.472 52.381 15.65 0.00 36.74 3.85
2262 2814 2.563702 GTCCCACGTGTAAAAACTCCA 58.436 47.619 15.65 0.00 0.00 3.86
2263 2815 2.944349 GTCCCACGTGTAAAAACTCCAA 59.056 45.455 15.65 0.00 0.00 3.53
2264 2816 2.944349 TCCCACGTGTAAAAACTCCAAC 59.056 45.455 15.65 0.00 0.00 3.77
2265 2817 2.946990 CCCACGTGTAAAAACTCCAACT 59.053 45.455 15.65 0.00 0.00 3.16
2266 2818 3.242936 CCCACGTGTAAAAACTCCAACTG 60.243 47.826 15.65 0.00 0.00 3.16
2267 2819 3.242936 CCACGTGTAAAAACTCCAACTGG 60.243 47.826 15.65 0.00 0.00 4.00
2268 2820 3.375922 CACGTGTAAAAACTCCAACTGGT 59.624 43.478 7.58 0.00 36.34 4.00
2269 2821 3.624410 ACGTGTAAAAACTCCAACTGGTC 59.376 43.478 0.00 0.00 36.34 4.02
2270 2822 3.302870 CGTGTAAAAACTCCAACTGGTCG 60.303 47.826 0.00 0.00 36.34 4.79
2271 2823 3.872771 GTGTAAAAACTCCAACTGGTCGA 59.127 43.478 0.00 0.00 36.34 4.20
2272 2824 4.514066 GTGTAAAAACTCCAACTGGTCGAT 59.486 41.667 0.00 0.00 36.34 3.59
2273 2825 4.753107 TGTAAAAACTCCAACTGGTCGATC 59.247 41.667 0.00 0.00 36.34 3.69
2274 2826 2.080286 AAACTCCAACTGGTCGATCG 57.920 50.000 9.36 9.36 36.34 3.69
2275 2827 1.254026 AACTCCAACTGGTCGATCGA 58.746 50.000 15.15 15.15 36.34 3.59
2276 2828 1.254026 ACTCCAACTGGTCGATCGAA 58.746 50.000 21.31 4.08 36.34 3.71
2277 2829 1.067776 ACTCCAACTGGTCGATCGAAC 60.068 52.381 26.11 26.11 36.34 3.95
2278 2830 0.245539 TCCAACTGGTCGATCGAACC 59.754 55.000 29.17 25.12 36.34 3.62
2279 2831 0.246635 CCAACTGGTCGATCGAACCT 59.753 55.000 29.17 12.45 0.00 3.50
2280 2832 1.337823 CCAACTGGTCGATCGAACCTT 60.338 52.381 29.17 17.58 0.00 3.50
2281 2833 1.993370 CAACTGGTCGATCGAACCTTC 59.007 52.381 29.17 12.17 0.00 3.46
2282 2834 0.531200 ACTGGTCGATCGAACCTTCC 59.469 55.000 29.17 20.71 0.00 3.46
2283 2835 0.530744 CTGGTCGATCGAACCTTCCA 59.469 55.000 29.17 23.85 0.00 3.53
2284 2836 0.530744 TGGTCGATCGAACCTTCCAG 59.469 55.000 29.17 0.00 0.00 3.86
2285 2837 0.806492 GGTCGATCGAACCTTCCAGC 60.806 60.000 22.68 4.95 0.00 4.85
2286 2838 0.806492 GTCGATCGAACCTTCCAGCC 60.806 60.000 21.31 0.00 0.00 4.85
2287 2839 1.218047 CGATCGAACCTTCCAGCCA 59.782 57.895 10.26 0.00 0.00 4.75
2288 2840 0.807667 CGATCGAACCTTCCAGCCAG 60.808 60.000 10.26 0.00 0.00 4.85
2289 2841 1.078143 ATCGAACCTTCCAGCCAGC 60.078 57.895 0.00 0.00 0.00 4.85
2290 2842 1.841302 ATCGAACCTTCCAGCCAGCA 61.841 55.000 0.00 0.00 0.00 4.41
2291 2843 1.377725 CGAACCTTCCAGCCAGCAT 60.378 57.895 0.00 0.00 0.00 3.79
2292 2844 1.372087 CGAACCTTCCAGCCAGCATC 61.372 60.000 0.00 0.00 0.00 3.91
2293 2845 0.034670 GAACCTTCCAGCCAGCATCT 60.035 55.000 0.00 0.00 0.00 2.90
2294 2846 0.034670 AACCTTCCAGCCAGCATCTC 60.035 55.000 0.00 0.00 0.00 2.75
2295 2847 1.153005 CCTTCCAGCCAGCATCTCC 60.153 63.158 0.00 0.00 0.00 3.71
2296 2848 1.523258 CTTCCAGCCAGCATCTCCG 60.523 63.158 0.00 0.00 0.00 4.63
2297 2849 2.249413 CTTCCAGCCAGCATCTCCGT 62.249 60.000 0.00 0.00 0.00 4.69
2298 2850 1.841302 TTCCAGCCAGCATCTCCGTT 61.841 55.000 0.00 0.00 0.00 4.44
2299 2851 1.817099 CCAGCCAGCATCTCCGTTC 60.817 63.158 0.00 0.00 0.00 3.95
2300 2852 2.169789 CAGCCAGCATCTCCGTTCG 61.170 63.158 0.00 0.00 0.00 3.95
2301 2853 3.567797 GCCAGCATCTCCGTTCGC 61.568 66.667 0.00 0.00 0.00 4.70
2302 2854 2.185350 CCAGCATCTCCGTTCGCT 59.815 61.111 0.00 0.00 34.29 4.93
2303 2855 1.437573 CCAGCATCTCCGTTCGCTA 59.562 57.895 0.00 0.00 32.29 4.26
2304 2856 0.872021 CCAGCATCTCCGTTCGCTAC 60.872 60.000 0.00 0.00 32.29 3.58
2305 2857 0.179137 CAGCATCTCCGTTCGCTACA 60.179 55.000 0.00 0.00 32.29 2.74
2306 2858 0.101399 AGCATCTCCGTTCGCTACAG 59.899 55.000 0.00 0.00 31.60 2.74
2307 2859 1.483424 GCATCTCCGTTCGCTACAGC 61.483 60.000 0.00 0.00 37.78 4.40
2334 2886 2.173669 CGTTCCTGCGTGGCCTATG 61.174 63.158 3.32 0.00 35.26 2.23
2358 2910 3.057736 GGCCTGCTGCATATACAAGATTG 60.058 47.826 1.31 0.00 43.89 2.67
2408 2960 3.323691 AGAAAAGCCCACCCAAACATAAC 59.676 43.478 0.00 0.00 0.00 1.89
2416 2968 4.466015 CCCACCCAAACATAACTGCTTTAT 59.534 41.667 0.00 0.00 0.00 1.40
2418 2970 6.153680 CCCACCCAAACATAACTGCTTTATAA 59.846 38.462 0.00 0.00 0.00 0.98
2444 2996 1.743996 AGAAAAATCTGAGCTCCGGC 58.256 50.000 12.15 0.00 39.06 6.13
2478 3030 0.822164 CCGTCGTCTCCCCAATTACT 59.178 55.000 0.00 0.00 0.00 2.24
2481 3033 1.138464 GTCGTCTCCCCAATTACTCCC 59.862 57.143 0.00 0.00 0.00 4.30
2502 3054 1.938577 CAGCCCTCACTGAATCGATTG 59.061 52.381 16.96 4.53 40.25 2.67
2508 3060 5.296780 GCCCTCACTGAATCGATTGATTTTA 59.703 40.000 16.96 2.21 44.79 1.52
2510 3062 6.414079 CCTCACTGAATCGATTGATTTTACG 58.586 40.000 16.96 0.00 44.79 3.18
2513 3065 5.449113 CACTGAATCGATTGATTTTACGCAC 59.551 40.000 16.96 0.00 44.79 5.34
2533 3085 2.166664 ACCTCTCTTCGCATTCTACACC 59.833 50.000 0.00 0.00 0.00 4.16
2587 3523 8.958119 AACGCAAGAATAATAGATGGAGTTAA 57.042 30.769 0.00 0.00 43.62 2.01
2588 3524 8.958119 ACGCAAGAATAATAGATGGAGTTAAA 57.042 30.769 0.00 0.00 43.62 1.52
2613 3549 3.658351 CTTTTAAGGAACGGATCTGCG 57.342 47.619 0.00 0.00 0.00 5.18
2636 3572 3.610911 CATTCCCTTAGTCTTCCACCAC 58.389 50.000 0.00 0.00 0.00 4.16
2637 3573 1.652947 TCCCTTAGTCTTCCACCACC 58.347 55.000 0.00 0.00 0.00 4.61
2638 3574 1.132657 TCCCTTAGTCTTCCACCACCA 60.133 52.381 0.00 0.00 0.00 4.17
2639 3575 1.003233 CCCTTAGTCTTCCACCACCAC 59.997 57.143 0.00 0.00 0.00 4.16
2640 3576 1.003233 CCTTAGTCTTCCACCACCACC 59.997 57.143 0.00 0.00 0.00 4.61
2641 3577 1.697432 CTTAGTCTTCCACCACCACCA 59.303 52.381 0.00 0.00 0.00 4.17
2665 3601 1.918800 AACGCCCCTGCTCTAGGTT 60.919 57.895 0.00 0.00 45.80 3.50
2684 3620 2.755103 GTTATCAGGTTTTGCCCTCAGG 59.245 50.000 0.00 0.00 38.26 3.86
2702 3638 1.891150 AGGAAATCAGTTTGCTGCAGG 59.109 47.619 17.12 0.00 43.31 4.85
2704 3640 1.888512 GAAATCAGTTTGCTGCAGGGA 59.111 47.619 17.12 0.00 42.29 4.20
2706 3642 1.471119 ATCAGTTTGCTGCAGGGATG 58.529 50.000 17.12 1.31 42.29 3.51
2710 3646 2.097825 AGTTTGCTGCAGGGATGAATC 58.902 47.619 17.12 0.00 0.00 2.52
2717 3653 1.064463 TGCAGGGATGAATCTGAACCC 60.064 52.381 0.00 0.00 40.71 4.11
2718 3654 1.752084 GCAGGGATGAATCTGAACCCC 60.752 57.143 0.00 0.00 41.26 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 1.202770 GCTTGGTGTAGTTCCCAGTGT 60.203 52.381 0.00 0.00 31.04 3.55
217 218 8.654485 AAAGGCATAATATATGGATGCTTTGA 57.346 30.769 21.29 0.00 42.85 2.69
273 274 3.448660 GGCATGGTAAGCTGGAAGAATTT 59.551 43.478 0.00 0.00 34.07 1.82
290 291 4.695217 ATTTACACTAAACGGTGGCATG 57.305 40.909 0.00 0.00 41.09 4.06
291 292 5.247084 TGTATTTACACTAAACGGTGGCAT 58.753 37.500 0.00 0.00 41.09 4.40
345 347 4.101274 ACTGATGCTAGCTTCATGACTGAT 59.899 41.667 27.76 5.26 31.27 2.90
390 395 9.921637 GAAATATTCTTTGTATTTGGTGGTGAA 57.078 29.630 0.00 0.00 33.23 3.18
396 401 9.533831 ACTGAGGAAATATTCTTTGTATTTGGT 57.466 29.630 0.00 0.00 33.23 3.67
467 475 2.741145 ACTAGAGTGATCCAGGTCCAC 58.259 52.381 0.00 6.03 0.00 4.02
531 539 3.125316 GTGCCTGAAGGAAATGTTACGAG 59.875 47.826 0.00 0.00 37.39 4.18
532 540 3.071479 GTGCCTGAAGGAAATGTTACGA 58.929 45.455 0.00 0.00 37.39 3.43
533 541 2.159707 CGTGCCTGAAGGAAATGTTACG 60.160 50.000 0.00 0.00 37.39 3.18
534 542 2.812011 ACGTGCCTGAAGGAAATGTTAC 59.188 45.455 0.00 0.00 37.39 2.50
535 543 2.811431 CACGTGCCTGAAGGAAATGTTA 59.189 45.455 0.82 0.00 37.39 2.41
536 544 1.608590 CACGTGCCTGAAGGAAATGTT 59.391 47.619 0.82 0.00 37.39 2.71
537 545 1.238439 CACGTGCCTGAAGGAAATGT 58.762 50.000 0.82 0.00 37.39 2.71
538 546 1.069022 CACACGTGCCTGAAGGAAATG 60.069 52.381 17.22 0.00 37.39 2.32
539 547 1.238439 CACACGTGCCTGAAGGAAAT 58.762 50.000 17.22 0.00 37.39 2.17
540 548 2.701587 CACACGTGCCTGAAGGAAA 58.298 52.632 17.22 0.00 37.39 3.13
541 549 4.454948 CACACGTGCCTGAAGGAA 57.545 55.556 17.22 0.00 37.39 3.36
579 587 4.320935 CGGTTGGGAAAGTAAAATGGACAG 60.321 45.833 0.00 0.00 0.00 3.51
583 591 4.038162 TGTTCGGTTGGGAAAGTAAAATGG 59.962 41.667 0.00 0.00 0.00 3.16
591 599 2.863740 GCTTTTTGTTCGGTTGGGAAAG 59.136 45.455 0.00 0.00 0.00 2.62
592 600 2.233922 TGCTTTTTGTTCGGTTGGGAAA 59.766 40.909 0.00 0.00 0.00 3.13
593 601 1.825474 TGCTTTTTGTTCGGTTGGGAA 59.175 42.857 0.00 0.00 0.00 3.97
594 602 1.475403 TGCTTTTTGTTCGGTTGGGA 58.525 45.000 0.00 0.00 0.00 4.37
596 604 5.975410 TTATTTGCTTTTTGTTCGGTTGG 57.025 34.783 0.00 0.00 0.00 3.77
600 608 7.183580 TGGATTTTATTTGCTTTTTGTTCGG 57.816 32.000 0.00 0.00 0.00 4.30
613 621 4.221924 CCCAAACGGACCTGGATTTTATTT 59.778 41.667 0.00 0.00 34.35 1.40
626 634 1.066454 CAACTCCAAACCCAAACGGAC 59.934 52.381 0.00 0.00 34.64 4.79
634 642 2.231716 ATTAGGGCAACTCCAAACCC 57.768 50.000 0.00 0.00 43.17 4.11
757 873 4.147449 TCGAGGGAGCGTGCATGG 62.147 66.667 8.27 0.00 0.00 3.66
1105 1247 1.291272 GACCGCCGACCTTGTACTT 59.709 57.895 0.00 0.00 0.00 2.24
1245 1390 2.725221 ATCAATGGAGCAGAAGACCC 57.275 50.000 0.00 0.00 0.00 4.46
1379 1528 2.351060 CGTCTCGTTGCAGTGGTAGTAA 60.351 50.000 0.00 0.00 0.00 2.24
1494 1643 1.001641 GGCCATCCTTGCAGTGTCT 60.002 57.895 0.00 0.00 0.00 3.41
1594 1743 1.670590 CCTGGCTCCGGAGATGATC 59.329 63.158 35.69 16.40 0.00 2.92
1715 1882 4.508662 AGCCTACACTAAGATTTGCTCAC 58.491 43.478 0.00 0.00 0.00 3.51
1749 1916 4.561606 GCACACCACATACTAACGAACTAG 59.438 45.833 0.00 0.00 0.00 2.57
1756 1923 2.156891 CACACGCACACCACATACTAAC 59.843 50.000 0.00 0.00 0.00 2.34
1762 1929 2.177394 TTATCACACGCACACCACAT 57.823 45.000 0.00 0.00 0.00 3.21
1835 2017 3.617540 TGTTGTTTACACATGCGAAGG 57.382 42.857 0.00 0.00 31.06 3.46
1871 2058 7.259882 TCGAACAGAGACACAAAGTAAAAGTA 58.740 34.615 0.00 0.00 0.00 2.24
1872 2059 6.103997 TCGAACAGAGACACAAAGTAAAAGT 58.896 36.000 0.00 0.00 0.00 2.66
1873 2060 6.583912 TCGAACAGAGACACAAAGTAAAAG 57.416 37.500 0.00 0.00 0.00 2.27
1874 2061 6.202188 GGATCGAACAGAGACACAAAGTAAAA 59.798 38.462 0.00 0.00 0.00 1.52
1875 2062 5.694910 GGATCGAACAGAGACACAAAGTAAA 59.305 40.000 0.00 0.00 0.00 2.01
1876 2063 5.221362 TGGATCGAACAGAGACACAAAGTAA 60.221 40.000 0.00 0.00 0.00 2.24
1877 2064 4.279922 TGGATCGAACAGAGACACAAAGTA 59.720 41.667 0.00 0.00 0.00 2.24
1878 2065 3.069586 TGGATCGAACAGAGACACAAAGT 59.930 43.478 0.00 0.00 0.00 2.66
1879 2066 3.653344 TGGATCGAACAGAGACACAAAG 58.347 45.455 0.00 0.00 0.00 2.77
1880 2067 3.320826 TCTGGATCGAACAGAGACACAAA 59.679 43.478 16.44 0.00 39.87 2.83
1899 2086 4.771590 TCAAGGCTGCATTTAGTTTCTG 57.228 40.909 0.50 0.00 0.00 3.02
1944 2445 9.528018 CAATTGTTCACCTGTAAGTTGTAAAAT 57.472 29.630 0.00 0.00 0.00 1.82
1958 2463 4.178540 CGTCGTATACCAATTGTTCACCT 58.821 43.478 4.43 0.00 0.00 4.00
1960 2465 4.622313 TCACGTCGTATACCAATTGTTCAC 59.378 41.667 4.43 0.00 0.00 3.18
1971 2476 0.827735 GTCGCGTTCACGTCGTATAC 59.172 55.000 5.77 0.00 42.22 1.47
1976 2483 4.986587 TGGGTCGCGTTCACGTCG 62.987 66.667 5.77 5.63 42.22 5.12
2045 2594 1.146358 GAGGGATGCTACGAACGTGC 61.146 60.000 10.14 11.33 0.00 5.34
2172 2724 9.406662 AGTGGGGATGAACTATTTAGGTATTAT 57.593 33.333 0.00 0.00 0.00 1.28
2173 2725 8.808240 AGTGGGGATGAACTATTTAGGTATTA 57.192 34.615 0.00 0.00 0.00 0.98
2174 2726 7.707467 AGTGGGGATGAACTATTTAGGTATT 57.293 36.000 0.00 0.00 0.00 1.89
2175 2727 8.826765 CATAGTGGGGATGAACTATTTAGGTAT 58.173 37.037 0.00 0.00 37.48 2.73
2176 2728 7.256547 GCATAGTGGGGATGAACTATTTAGGTA 60.257 40.741 0.00 0.00 37.48 3.08
2177 2729 6.465894 GCATAGTGGGGATGAACTATTTAGGT 60.466 42.308 0.00 0.00 37.48 3.08
2178 2730 5.940470 GCATAGTGGGGATGAACTATTTAGG 59.060 44.000 0.00 0.00 37.48 2.69
2179 2731 6.773638 AGCATAGTGGGGATGAACTATTTAG 58.226 40.000 0.00 0.00 37.48 1.85
2180 2732 6.763715 AGCATAGTGGGGATGAACTATTTA 57.236 37.500 0.00 0.00 37.48 1.40
2181 2733 5.653255 AGCATAGTGGGGATGAACTATTT 57.347 39.130 0.00 0.00 37.48 1.40
2182 2734 6.959606 ATAGCATAGTGGGGATGAACTATT 57.040 37.500 0.00 0.00 37.48 1.73
2183 2735 6.959606 AATAGCATAGTGGGGATGAACTAT 57.040 37.500 0.00 0.00 39.62 2.12
2184 2736 6.558775 AGAAATAGCATAGTGGGGATGAACTA 59.441 38.462 0.00 0.00 33.59 2.24
2185 2737 5.370880 AGAAATAGCATAGTGGGGATGAACT 59.629 40.000 0.00 0.00 0.00 3.01
2186 2738 5.471456 CAGAAATAGCATAGTGGGGATGAAC 59.529 44.000 0.00 0.00 0.00 3.18
2187 2739 5.132648 ACAGAAATAGCATAGTGGGGATGAA 59.867 40.000 0.00 0.00 0.00 2.57
2188 2740 4.660303 ACAGAAATAGCATAGTGGGGATGA 59.340 41.667 0.00 0.00 0.00 2.92
2189 2741 4.978099 ACAGAAATAGCATAGTGGGGATG 58.022 43.478 0.00 0.00 0.00 3.51
2190 2742 5.132648 TCAACAGAAATAGCATAGTGGGGAT 59.867 40.000 0.00 0.00 0.00 3.85
2191 2743 4.473196 TCAACAGAAATAGCATAGTGGGGA 59.527 41.667 0.00 0.00 0.00 4.81
2192 2744 4.576463 GTCAACAGAAATAGCATAGTGGGG 59.424 45.833 0.00 0.00 0.00 4.96
2193 2745 5.185454 TGTCAACAGAAATAGCATAGTGGG 58.815 41.667 0.00 0.00 0.00 4.61
2194 2746 6.722301 CATGTCAACAGAAATAGCATAGTGG 58.278 40.000 0.00 0.00 0.00 4.00
2195 2747 6.183360 TGCATGTCAACAGAAATAGCATAGTG 60.183 38.462 0.00 0.00 0.00 2.74
2196 2748 5.882000 TGCATGTCAACAGAAATAGCATAGT 59.118 36.000 0.00 0.00 0.00 2.12
2197 2749 6.367686 TGCATGTCAACAGAAATAGCATAG 57.632 37.500 0.00 0.00 0.00 2.23
2198 2750 5.220912 GCTGCATGTCAACAGAAATAGCATA 60.221 40.000 9.76 0.00 35.90 3.14
2199 2751 4.439700 GCTGCATGTCAACAGAAATAGCAT 60.440 41.667 9.76 0.00 35.90 3.79
2200 2752 3.119743 GCTGCATGTCAACAGAAATAGCA 60.120 43.478 9.76 0.00 35.90 3.49
2201 2753 3.432782 GCTGCATGTCAACAGAAATAGC 58.567 45.455 9.76 0.00 35.90 2.97
2202 2754 3.693085 AGGCTGCATGTCAACAGAAATAG 59.307 43.478 0.50 0.00 35.90 1.73
2203 2755 3.689347 AGGCTGCATGTCAACAGAAATA 58.311 40.909 0.50 0.00 35.90 1.40
2204 2756 2.522185 AGGCTGCATGTCAACAGAAAT 58.478 42.857 0.50 0.00 35.90 2.17
2205 2757 1.985473 AGGCTGCATGTCAACAGAAA 58.015 45.000 0.50 0.00 35.90 2.52
2206 2758 2.857186 TAGGCTGCATGTCAACAGAA 57.143 45.000 0.50 0.00 35.90 3.02
2207 2759 2.420547 GGATAGGCTGCATGTCAACAGA 60.421 50.000 12.84 0.00 35.90 3.41
2208 2760 1.945394 GGATAGGCTGCATGTCAACAG 59.055 52.381 12.84 2.58 36.96 3.16
2209 2761 1.281577 TGGATAGGCTGCATGTCAACA 59.718 47.619 12.84 0.18 0.00 3.33
2210 2762 1.672881 GTGGATAGGCTGCATGTCAAC 59.327 52.381 12.84 8.03 0.00 3.18
2211 2763 1.281577 TGTGGATAGGCTGCATGTCAA 59.718 47.619 12.84 0.00 0.00 3.18
2212 2764 0.911053 TGTGGATAGGCTGCATGTCA 59.089 50.000 12.84 0.00 0.00 3.58
2213 2765 2.149578 GATGTGGATAGGCTGCATGTC 58.850 52.381 2.28 2.28 0.00 3.06
2214 2766 1.491754 TGATGTGGATAGGCTGCATGT 59.508 47.619 0.50 0.00 0.00 3.21
2215 2767 2.265589 TGATGTGGATAGGCTGCATG 57.734 50.000 0.50 0.00 0.00 4.06
2216 2768 2.374170 TGATGATGTGGATAGGCTGCAT 59.626 45.455 0.50 0.00 0.00 3.96
2217 2769 1.770061 TGATGATGTGGATAGGCTGCA 59.230 47.619 0.50 0.00 0.00 4.41
2218 2770 2.224475 ACTGATGATGTGGATAGGCTGC 60.224 50.000 0.00 0.00 0.00 5.25
2219 2771 3.766068 ACTGATGATGTGGATAGGCTG 57.234 47.619 0.00 0.00 0.00 4.85
2220 2772 3.256879 CGTACTGATGATGTGGATAGGCT 59.743 47.826 0.00 0.00 0.00 4.58
2221 2773 3.005897 ACGTACTGATGATGTGGATAGGC 59.994 47.826 0.00 0.00 0.00 3.93
2222 2774 4.321304 GGACGTACTGATGATGTGGATAGG 60.321 50.000 0.00 0.00 0.00 2.57
2223 2775 4.321304 GGGACGTACTGATGATGTGGATAG 60.321 50.000 0.00 0.00 0.00 2.08
2224 2776 3.572682 GGGACGTACTGATGATGTGGATA 59.427 47.826 0.00 0.00 0.00 2.59
2225 2777 2.365617 GGGACGTACTGATGATGTGGAT 59.634 50.000 0.00 0.00 0.00 3.41
2226 2778 1.754803 GGGACGTACTGATGATGTGGA 59.245 52.381 0.00 0.00 0.00 4.02
2227 2779 1.480545 TGGGACGTACTGATGATGTGG 59.519 52.381 0.00 0.00 0.00 4.17
2228 2780 2.540515 GTGGGACGTACTGATGATGTG 58.459 52.381 0.00 0.00 0.00 3.21
2229 2781 1.134367 CGTGGGACGTACTGATGATGT 59.866 52.381 0.00 0.00 36.74 3.06
2230 2782 1.840181 CGTGGGACGTACTGATGATG 58.160 55.000 0.00 0.00 36.74 3.07
2242 2794 2.563702 TGGAGTTTTTACACGTGGGAC 58.436 47.619 21.57 10.28 0.00 4.46
2243 2795 2.944349 GTTGGAGTTTTTACACGTGGGA 59.056 45.455 21.57 4.16 0.00 4.37
2244 2796 2.946990 AGTTGGAGTTTTTACACGTGGG 59.053 45.455 21.57 0.00 0.00 4.61
2245 2797 3.242936 CCAGTTGGAGTTTTTACACGTGG 60.243 47.826 21.57 1.66 37.39 4.94
2246 2798 3.375922 ACCAGTTGGAGTTTTTACACGTG 59.624 43.478 15.48 15.48 38.94 4.49
2247 2799 3.613030 ACCAGTTGGAGTTTTTACACGT 58.387 40.909 4.92 0.00 38.94 4.49
2248 2800 3.302870 CGACCAGTTGGAGTTTTTACACG 60.303 47.826 4.92 0.00 38.94 4.49
2249 2801 3.872771 TCGACCAGTTGGAGTTTTTACAC 59.127 43.478 4.92 0.00 38.94 2.90
2250 2802 4.139859 TCGACCAGTTGGAGTTTTTACA 57.860 40.909 4.92 0.00 38.94 2.41
2251 2803 4.143179 CGATCGACCAGTTGGAGTTTTTAC 60.143 45.833 10.26 0.00 38.94 2.01
2252 2804 3.991773 CGATCGACCAGTTGGAGTTTTTA 59.008 43.478 10.26 0.00 38.94 1.52
2253 2805 2.806244 CGATCGACCAGTTGGAGTTTTT 59.194 45.455 10.26 0.00 38.94 1.94
2254 2806 2.036733 TCGATCGACCAGTTGGAGTTTT 59.963 45.455 15.15 0.00 38.94 2.43
2255 2807 1.616865 TCGATCGACCAGTTGGAGTTT 59.383 47.619 15.15 0.00 38.94 2.66
2256 2808 1.254026 TCGATCGACCAGTTGGAGTT 58.746 50.000 15.15 0.00 38.94 3.01
2257 2809 1.067776 GTTCGATCGACCAGTTGGAGT 60.068 52.381 19.26 0.00 38.94 3.85
2258 2810 1.630148 GTTCGATCGACCAGTTGGAG 58.370 55.000 19.26 0.00 38.94 3.86
2259 2811 0.245539 GGTTCGATCGACCAGTTGGA 59.754 55.000 19.26 0.00 38.94 3.53
2260 2812 0.246635 AGGTTCGATCGACCAGTTGG 59.753 55.000 27.25 0.00 42.17 3.77
2261 2813 1.993370 GAAGGTTCGATCGACCAGTTG 59.007 52.381 27.25 0.00 0.00 3.16
2262 2814 1.067071 GGAAGGTTCGATCGACCAGTT 60.067 52.381 27.25 18.47 0.00 3.16
2263 2815 0.531200 GGAAGGTTCGATCGACCAGT 59.469 55.000 27.25 18.98 0.00 4.00
2264 2816 0.530744 TGGAAGGTTCGATCGACCAG 59.469 55.000 27.25 0.00 0.00 4.00
2265 2817 0.530744 CTGGAAGGTTCGATCGACCA 59.469 55.000 27.25 23.76 0.00 4.02
2266 2818 0.806492 GCTGGAAGGTTCGATCGACC 60.806 60.000 19.26 20.83 0.00 4.79
2267 2819 0.806492 GGCTGGAAGGTTCGATCGAC 60.806 60.000 19.26 12.82 0.00 4.20
2268 2820 1.254975 TGGCTGGAAGGTTCGATCGA 61.255 55.000 15.15 15.15 0.00 3.59
2269 2821 0.807667 CTGGCTGGAAGGTTCGATCG 60.808 60.000 9.36 9.36 0.00 3.69
2270 2822 1.092345 GCTGGCTGGAAGGTTCGATC 61.092 60.000 0.00 0.00 0.00 3.69
2271 2823 1.078143 GCTGGCTGGAAGGTTCGAT 60.078 57.895 0.00 0.00 0.00 3.59
2272 2824 1.841302 ATGCTGGCTGGAAGGTTCGA 61.841 55.000 0.00 0.00 0.00 3.71
2273 2825 1.372087 GATGCTGGCTGGAAGGTTCG 61.372 60.000 0.00 0.00 0.00 3.95
2274 2826 0.034670 AGATGCTGGCTGGAAGGTTC 60.035 55.000 0.00 0.00 0.00 3.62
2275 2827 0.034670 GAGATGCTGGCTGGAAGGTT 60.035 55.000 0.00 0.00 0.00 3.50
2276 2828 1.606531 GAGATGCTGGCTGGAAGGT 59.393 57.895 0.00 0.00 0.00 3.50
2277 2829 1.153005 GGAGATGCTGGCTGGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
2278 2830 1.523258 CGGAGATGCTGGCTGGAAG 60.523 63.158 0.00 0.00 0.00 3.46
2279 2831 1.841302 AACGGAGATGCTGGCTGGAA 61.841 55.000 0.00 0.00 0.00 3.53
2280 2832 2.244117 GAACGGAGATGCTGGCTGGA 62.244 60.000 0.00 0.00 0.00 3.86
2281 2833 1.817099 GAACGGAGATGCTGGCTGG 60.817 63.158 0.00 0.00 0.00 4.85
2282 2834 2.169789 CGAACGGAGATGCTGGCTG 61.170 63.158 0.00 0.00 0.00 4.85
2283 2835 2.185350 CGAACGGAGATGCTGGCT 59.815 61.111 0.00 0.00 0.00 4.75
2284 2836 2.629050 TAGCGAACGGAGATGCTGGC 62.629 60.000 0.00 0.00 38.33 4.85
2285 2837 0.872021 GTAGCGAACGGAGATGCTGG 60.872 60.000 0.00 0.00 38.33 4.85
2286 2838 0.179137 TGTAGCGAACGGAGATGCTG 60.179 55.000 0.00 0.00 38.33 4.41
2287 2839 0.101399 CTGTAGCGAACGGAGATGCT 59.899 55.000 0.00 0.00 41.32 3.79
2288 2840 1.483424 GCTGTAGCGAACGGAGATGC 61.483 60.000 5.37 0.00 36.47 3.91
2289 2841 2.582959 GCTGTAGCGAACGGAGATG 58.417 57.895 5.37 0.00 36.47 2.90
2309 2861 4.379243 ACGCAGGAACGGAGCAGG 62.379 66.667 0.00 0.00 37.37 4.85
2310 2862 3.114616 CACGCAGGAACGGAGCAG 61.115 66.667 0.00 0.00 37.37 4.24
2311 2863 4.680237 CCACGCAGGAACGGAGCA 62.680 66.667 0.00 0.00 41.22 4.26
2331 2883 2.371510 TGTATATGCAGCAGGCCACATA 59.628 45.455 5.01 5.22 43.89 2.29
2334 2886 1.605710 CTTGTATATGCAGCAGGCCAC 59.394 52.381 5.01 0.00 43.89 5.01
2358 2910 0.811281 GTGTTAGCAGATGGGCCAAC 59.189 55.000 11.89 8.41 36.20 3.77
2375 2927 1.478105 GGGCTTTTCTTAGGGCATGTG 59.522 52.381 0.00 0.00 0.00 3.21
2418 2970 7.255277 GCCGGAGCTCAGATTTTTCTATTAAAT 60.255 37.037 17.19 0.00 35.50 1.40
2461 3013 1.138464 GGGAGTAATTGGGGAGACGAC 59.862 57.143 0.00 0.00 0.00 4.34
2468 3020 1.230212 GGCTGGGGAGTAATTGGGG 59.770 63.158 0.00 0.00 0.00 4.96
2478 3030 1.229951 ATTCAGTGAGGGCTGGGGA 60.230 57.895 0.00 0.00 37.12 4.81
2481 3033 0.467384 ATCGATTCAGTGAGGGCTGG 59.533 55.000 0.00 0.00 37.12 4.85
2502 3054 2.029365 GCGAAGAGAGGTGCGTAAAATC 59.971 50.000 0.00 0.00 0.00 2.17
2508 3060 0.737715 GAATGCGAAGAGAGGTGCGT 60.738 55.000 0.00 0.00 0.00 5.24
2510 3062 2.197577 GTAGAATGCGAAGAGAGGTGC 58.802 52.381 0.00 0.00 0.00 5.01
2513 3065 2.166459 TGGTGTAGAATGCGAAGAGAGG 59.834 50.000 0.00 0.00 0.00 3.69
2598 3534 2.125106 GGCGCAGATCCGTTCCTT 60.125 61.111 10.83 0.00 0.00 3.36
2608 3544 0.178068 GACTAAGGGAATGGCGCAGA 59.822 55.000 10.83 0.00 0.00 4.26
2609 3545 0.179000 AGACTAAGGGAATGGCGCAG 59.821 55.000 10.83 0.00 0.00 5.18
2613 3549 2.644676 GTGGAAGACTAAGGGAATGGC 58.355 52.381 0.00 0.00 0.00 4.40
2636 3572 2.049767 GGGGCGTTGGTTATGGTGG 61.050 63.158 0.00 0.00 0.00 4.61
2637 3573 1.001393 AGGGGCGTTGGTTATGGTG 60.001 57.895 0.00 0.00 0.00 4.17
2638 3574 1.001393 CAGGGGCGTTGGTTATGGT 60.001 57.895 0.00 0.00 0.00 3.55
2639 3575 2.414785 GCAGGGGCGTTGGTTATGG 61.415 63.158 0.00 0.00 0.00 2.74
2640 3576 3.196648 GCAGGGGCGTTGGTTATG 58.803 61.111 0.00 0.00 0.00 1.90
2665 3601 2.274542 TCCTGAGGGCAAAACCTGATA 58.725 47.619 0.00 0.00 42.10 2.15


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.